Bioinformatics meetings & conferences

ACM Sixth International Workshop on Data and Text Mining in Biomedical Informatics (DTMBIO)

October 29, 2012

In conjunction with ACM 20th Conference on Information and Knowledge Management (CIKM) Maui, Hawaii, USA

October 29-November 2, 2012

DTMBIO 12 organizers are pleased to announce that the sixth DTMBIO will be held in conjunction with CIKM, one of the largest data and text mining conferences. While CIKM presents the state-of-the-art research in informatics with the primary focus on data and text mining, the main focus of DTMBIO is on biomedical and healthcare informatics. DTMBIO delegates will bring forth interesting applications of up-to-date informatics in the context of biomedical research.

Biological researchers face the current challenge of making effective use of the enormous amount of electronic biomedical data in order to better understand and explain complex biological systems. The biomedical data repositories include data in a wide variety of forms, including bibliographic information from electronic medical journals, gene expression data from Microarray experiments, protein identification and quantification data from proteomics experiments, genomic sequences gathered by the Human Genome Project, and patient healthcare records. The ability to automatically and effectively extract, integrate, understand and make use of information embedded in such heterogeneous - structured and unstructured - data remains a challenging task.

Topic of Interest
The relevant topics include the following (but not limited to):

- Proposal and assessment of novel Text Mining (TM) evaluation
- Evaluation methods of biomedical applications, shared tasks
- Biomedical and Clinical text mining applications
- Information extraction from biomedical and clinical corpora (full texts, abstracts, EHRs, clinical trials, etc)
- Information retrieval from large biomedical data collections
- Gene sequence annotation
- Protein/RNA structure prediction
- Medical Ontologies and Text Mining
- Sequence and structural motifs
- Modeling of biochemical pathways and biological networks
- Image Mining in Medical and healthcare informatics
- Data and Text Mining solutions in biomedical informatics, for applications such as drug development, system biology, biomedical working processes
- Information integration for Data and Text Mining
- Mining multi-relational data

International Conference in Modeling Health Advances (ICMHA'12)

San Francisco, USA, 24-26 October, 2012

The International Conference in Modeling Health Advances 2012 will take place in San Francisco, USA, 24-26 October, 2012.

A host of new diseases, like HIV/AIDS, BSE, Avian Flu, West Nile Virus and others have appeared on the scene during the last twenty five years and undoubtedly, more will come in the coming years. To tackle these illnesses, the cooperation of modelers, mathematicians, statisticians, computer scientists, and others, and of researchers from the medical community is absolutely essential. Modeling is important because it gives important insight into the method of treatment. In the case of HIV/AIDS, for example, mathematical modeling indicated that a combination of both protease inhibitors and reverse transcriptase inhibitors would be far more effective than any one of these two drugs.

The purpose of this conference is to bring all the people working in the area of epidemiology under one roof and encourage mutual interaction.

The conference ICMHA'12 is held under the World Congress on Engineering and Computer Science WCECS 2012. The WCECS 2012 is organized by the International Association of Engineers (IAENG), a non-profit international association for engineers and computer scientists. The congress has the focus on the frontier topics in the theoretical and applied engineering and computer science subjects. The last IAENG conference has attracted more than five hundred participants from over 30 countries. All submitted papers will be under peer review and accepted papers will be published in the conference proceeding (ISBN: 978-988-19251-6-9). The abstracts will be indexed and available at major academic databases. The accepted papers will also be considered for publication in the special issues of the journal Engineering Letters, in IAENG journals and in edited books by publishers like Springer.

Genome Informatics Workshop 2012

December 12-14, 2012 Tainan, Taiwan

Genome Informatics Workshop (GIW) is the longest running international bioinformatics conference in the world. The scope includes all works that are ultimately devoted to the computational understanding of biological systems on the molecular basis and the aims are to present recent results of both theoretical and practical research, to demonstrate biological systems, and to show new applications and directions of future research. The first GIW was held at Tokyo in 1990. Since then, GIW has been held annually around the countries in Asia-Pacific region. This year's GIW is the 23rd anniversary and will be held at Tainan in Taiwan. The purpose of GIW2012 is to provide an international forum for scientists and researchers to exchange ideas and approaches.

National Cheng Kung University and Taiwan Society for Bioinformatics and Systems Biology (TSBSB) are honored to host the GIW2012. We are delighted to give you a warm welcome to Tainan in Taiwan.

International Federation for Information Processing/International Medical Informatics Association International Working Conference on Interfacing Bio- and Medical Informatics

27 September 2012 Amsterdam, the Netherlands

From 24 to 26 September 2012 the International Federation for Information Processing (IFIP) is having its World Computer Congress WCC2012 in Amsterdam, the Netherlands (www.wcc-2012.org). During the WCC2010 conference in Brisbane, Australia, IFIP and the International Medical Informatics Association (IMIA) organized a joint conference for the first time in their history. Also this time a joint one-day associated meeting will be held on Thursday 27 September. The topic of this meeting will be the link between bioinformatics and medical informatics. IFIP’s Working Groups 5.13 Bioinformatics and its applications and IMIA’s Working Group on Informatics in Genomic Medicine (IGM) are working in this area and supporting this event.

Contact
Prof.dr. Arie Hasman e-mail: a.hasman@amc.uva.nl

Conference topics

Applications:

Personalized medicine

Cancer informatics

Population genetics

Bioinformatics approaches for diseases study

Genomics and proteomics in medicine

Analysis of gene expression, mutation, variations and next generation sequencing

Linking genotype with phenotype

Tools:

Databases, data management and integration

Query languages, information retrieval, interoperability, biomedical ontologies and semantics

Knowledge discovery, machine learning, pattern recognition and text mining

Data visualization

High-performance, grid and cloud computing

Statistical Bioinformatics - Approaches to the Challenges of High-Dimensional Data

Tuesday 26th June 2012 Leeds, United Kingdom

The Statistical bioinformatics - Approaches to the challenges of high-dimensional data Workshop 2012 will be held on Tuesday 26th June 2012 in Leeds.

The workshop will be the opportunity for statisticians, epidemiologists, bioinformatics analysts and laboratory scientists to attend a highly relevant meeting and network with colleague from relevant research areas. The workshop will bring together experts in the field to discuss current research and future directions of statistical bioinformatics and the analysis of high dimensional data.

The event is supported by the World Universities Network and will take place within the Faculty of Medicine and Health, room 8.34 on level 8 of the Worsley Building, University of Leeds, UK.

If you have further questions about the conference please contact the conference administrator Sou Sit Chung: s.chung@leeds.ac.uk.

Markers in Cancer 2012

October 11-13, 2012 Holywood, Florida

Markers in Cancer 2012 (formerly known as the ASCO-NCI-EORTC Annual Meeting on Molecular Markers in Cancer) will stimulate discussion on the use of biomarkers as a tool for optimizing detection and treatment in oncology.

Designed for clinicians, pathologists, clinical and translational researchers, statisticians, radiologists, and others who specialize in molecular diagnostics, the meeting will present the latest advances in cancer markers to assess drug efficacy, improve prognostic and predictive evaluations and imaging, and enhance clinical trial development.

This year's Meeting will focus on practice-oriented translational research. Join us in Florida to review and explore the latest innovations in cancer markers.

Annual Biomedical Research Conference for Minority Students

November 7-10, 2012 San Jose, California

ABRCMS
American Society for Microbiology Education Department
1752 N Street, NW
Washington, DC 20036

Ph: 202-942-9348
Fax: 202-403-3513

Email:abrcms@asmusa.org

Fifth International Symposium on Semantic Mining in Biomedicine (SMBM 2012)

September 3rd and 4th, 2012 Institute of Computational Linguistics, University of Zurich, Switzerland

The 5th International Symposium on Semantic Mining in Biomedicine (SMBM) 3rd-4th September, 2012 will be held at the Institute of Computational Linguistics, University of Zurich, Switzerland. Support is provided by the projects SASEBio/OntoGene (SNF105315_130558/1) and MANTRA (EU FP7).

SMBM 2012 aims to bring together researchers from text and data mining in biomedicine, medical, bio- and chemoinformatics, and researchers from biomedical ontology design and engineering.

SMBM 2012 is the follow-up event of SMBM 2010 (EBI, U.K.), SMBM 2008 (University of Turku, Finland), SMBM 2006 (University of Jena, Germany), and SMBM 2005 (EBI, U.K.).

Selected papers will be considered for publication in a special issue of the Journal of Biomedical Semantics (JBMS).

[contact the organization committee via smbmzurich @ gmail.com]

Mathematical and Computational Medicine Conference 2012

Saturday December 1 2012 - Wednesday December 5 2012 Xcaret, Mexico

The purpose of the Zing Conference on Mathematical and Computational Medicine is to bring together eminent scholars with expertise in various fields of mathematical and computational medicine, as well as experimentalists and medical doctors interested in application of computational methods in clinical studies. The mathematical and computational medicine is now one of the most important and rapidly growing fields of modern medicine, and will become even more important in nearest future, when the cost of individual human gene sequencing becomes affordable for mass-scale clinical use (The $1000 Human Genome). New sequencing techniques, such as RNA-Seq produce enormous amount of information on the transcriptome in healthy and diseased cells, that need a development of new mathematical and computational methods to extract the most important medical information. The scope of the proposed Zing Conference will cover many different fields mathematical and computational medicine and biomedical informatics, such as genetics, genomics, epigenetics, and epigenomics of various diseases including mental and learning disorders, autism, and somatic diseases, with a special emphasis on cancer, protein misfolding disorders related to amyloid formation in neurogenerative diseases (such as Alzheimer's and Parkinson's disease), gene regulation, biomarker development, computer aided drug development, computational pharmacodynamics, computational immunology, systems biology and its extension to systems medicine, machine learning methods in application to biomedical data, applicability of computational methods in personalized medicine, and regenerative medicine. A special session will be devoted to errors in measurements of biomedical data and statistical evidence-based medicine.

For general queries about conference attendance, registration, payment, accommodation, etc. please email info~at~zingconferences.com (replace '~at~' with '@').

13th Annual Bioinformatics Open Source Conference (BOSC 2012)

The 13th Annual Bioinformatics Open Source Conference (BOSC 2012) will take place July 13-14, 2012, in Long Beach, CA, right before ISMB 2012.

The Bioinformatics Open Source Conference (BOSC) is sponsored by the Open Bioinformatics Foundation (O|B|F), a non-profit group dedicated to promoting the practice and philosophy of Open Source software development within the biological research community.

Open Source software has flourished in the bioinformatics community for well over a decade. When the first BOSC (Bioinformatics Open Source Conference) was held in 2000, there were already a number of popular open source bioinformatics packages, and the number and range of these projects has increased dramatically since then. Many open source bioinformatics packages are widely used by the research community across a wide variety of applications. Open source bioinformatics software has facilitated rapid innovation, dissemination, and wide adoption of new computational methods, reusable software components, and standards.

BOSC brings together bioinformatics open source developers from all over the world so they can forge connections each other (both within and across projects), increase the visibility of their work, and collaborate to build shared resources. Participants can work together to create use cases, prototype working code, or run hands-on tutorials in new software packages and emerging technologies. For those who are bioinformatics software users rather than developers, BOSC introduces or updates them on a wide array of projects that they might find useful.

Sessions

Cloud and Parallel Computing -- This session will cover cloud-based approaches to improving software and data accessibility. The emergence of cloud computing has made highly scalable cluster computing available to computational biologists. Services such as Amazon's Elastic Compute Cloud combined with publicly available datasets promise to lower the overhead to participate in large scale data analyses. Talks will focus on how the community can build up resources, datasets, and workflows for making the best use of cloud infrastructure. We will also include talks on data-parallel approaches to analyzing massive data sets, such as those resulting from next-generation sequencing and mass spec proteomics, and reports on the parallelization of bioinformatics algorithms in general.

Linked Data -- Linked Data is an emerging set of conventions on using basic Semantic Web standards (HTTP URIs and RDF in particular) to expose, share, and connect data, information, and knowledge online. Linked Data principles are increasingly being embraced by bioinformatics resources. For example, UniProt is now being made fully available in RDF , and collaborative initiatives such as Bio2RDF aim to expose many commonly used database resources to data integration through RDF and its query language, SPARQL. This session is devoted to reports on software that works with such new data stores, or aids in their development, including technologies for interoperable web services, and tools for ontology building or maintenance.

Genome-scale Data Management -- This session will focus on processes and technologies that support the creating, managing and reporting of genomic data. This session is appropriate for discussion of systems that involve components such as (but not limited to) Ensembl and GMOD/Chado data stores, Taverna and Galaxy analysis workflows, and BioMart and InterMine warehouses.

Data Visualization and Imaging -- This session will address visualization techniques and tools that provide insight into large and highly complex biomedical data sets , as well as biological image processing, analysis and data management. Talks that address the development of frameworks and communities are particularly welcome.

Translational Bioinformatics -- This session will explore applications of biological and medical informatics to the development of personalized healthcare, therapies, and a better understanding of human health and disease. Topics include the analysis of human microarray and other 'omics data, bioinformatics methodologies for clinical research, and tools for discovering clinically useful associations in human databases.

Bioinformatics Open Source Project Updates -- This session will feature short talks from ongoing projects describing their recent progress. Abstracts will be solicited from open source projects affiliated with the O|B|F (see http://www.open-bio.org/wiki/Projects), including the Bio projects, DAS, BioMOBY, EMBOSS, and GMOD, but any other open-source project will be equally eligible to submit presentations for this session.

Panel: Interfacing with Industry -- Companies are more and more seeing the benefits of working with open source code and making their own code open; meanwhile, academics frequently partner with companies on their research projects. We encourage submissions from companies that work with open source software, as well as developers from non-commercial organizations who collaborate with companies. We anticipate a broadly useful conversation about the benefits and pitfalls of academic/commercial interaction.